Vector RAG vs LLM-Compiled Wiki: A Preregistered Comparison on a Small Multi-Domain Research

Scientific question answering requires a retrieval system to solve two distinct problems: identifying which papers are relevant and locating the supporting evidence within those papers. Conventional retrieval-augmented generation typically addresses both through similarity search over fixed-length passages, flattening document structure and separating scientific claims from their methodological and argumentative context. We present VecTree-RAG, an agentic framework that assigns these tasks to complementary retrieval mechanisms. Vector search ranks compact document and section representations across the corpus, whereas reasoning-guided traversal of source-verified section trees localizes evidence within shortlisted papers. Full text is retained in a page store and exposed progressively only after structural localization. We evaluate VecTree-RAG on 300 QASPER questions, an open-access subset of 54 LitQA2 questions, and 49 multi-document MOSAIC questions. Compared with Dense RAG, reranked Dense RAG, RAPTOR, and Search-o1, VecTree-RAG obtained the highest observed answer score on all three benchmarks, reaching 0.800 LLM-judge correctness on QASPER, 0.925 accuracy on LitQA2, and a 0.547 composite score on MOSAIC. On QASPER, its evidence-page precision was 0.274, compared with 0.046--0.071 for the baselines. LitQA2 ablations further showed that the complete vector--tree architecture required fewer inference tokens than variants without tree navigation or corpus-level vector routing. These results indicate that vector retrieval narrows the corpus-level search space and tree navigation concentrates reading on structurally relevant evidence. Although multi-turn inference remains more expensive than single-call retrieval, VecTree-RAG provides a structure-aware and traceable architecture for scientific literature question answering.

The LLM Wiki pattern, to compile and provide domain knowledge into a persistent artifact and serve it to LLMs via KV cache inference, promises context access at sub-second latency with zero retrieval failure. Realizing this requires solving the compilation gap: LLM compilation distilling raw documents into a wiki without catastrophically discarding critical facts. We characterize this gap across 17 RepLiQA domains (6,800 questions): we observe that full context KV cache inference outperforms RAG on curated knowledge (4.38 vs. 4.08 out of 5, 7.3 faster TTFT) but degrades below RAG at scale due to attention dilution, and blind compilation fails entirely (2.14 to 2.32 vs. 3.46, 53 to 60% catastrophic failure rate). To address the compilation gap, we propose WiCER (Wiki-memory Compile, Evaluate, Refine), an iterative algorithm inspired by counterexample-guided abstraction refinement (CEGAR) that closes this gap. WiCER evaluates compiled wikis against diagnostic probes, identifies dropped facts, and forces their preservation in subsequent compilations. One to two iterations recover 80% of lost quality (mean 3.24 vs. 3.47 for raw full-context across the 15 topics with baselines), reducing catastrophic failures by 55% relative. An ablation across all 17 topics confirms that targeted diagnosis (+0.95), not generic pinning (+0.16), drives the gains. All code and benchmarks are released for reproducible research.

Retrieval-augmented generation (RAG) systems are often compared by asking a large language model (LLM) judge which answer is better. For multi-hop RAG, this has become a measurement problem as much as a modeling problem: the same score can reflect retrieval quality, answer length, lexical overlap, or a statistical test that ignores clustered data. We ask what happens when these choices are made explicit. We propose a minimum measurement standard for LLM-as-a-judge comparisons in RAG. The standard fixes the top-100 candidate pool, evidence budget, answer cap, generator, and prompt; it also requires pre-registered hypotheses, cluster-aware inference, an exact cluster sign-flip check when feasible, and second-judge replication. Clustered benchmarks can overstate progress; the field should adopt this standard. We stress-test it with Genetic Algorithm Decoder for Multi-hop Evidence Composition (GADMEC), an evolutionary evidence selector, on 400 multi-hop questions in computer science/machine learning (CS/ML) and Materials Science. The protocol changes the empirical story. A binomial test makes all four semantic-baseline comparisons look significant; cluster-aware inference leaves only one Bonferroni-significant result. BM25 beats pure semantic GADMEC under the same budget, while a lexical-semantic hybrid recovers in CS/ML and narrows the Materials Science gap.